The creationists are gonna freak!

[NobbyNobbs]

I stumbled across this (http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html)today, and would like verification. Specifically, I'm not familiar with New Scientist magazine, and I don't know how reliable a source they are. Would anyone care to comment?

[Denver]

That' s a cool article. I don't think it will phase most branches of creationism though. It's the 'beginning' that creationism mostly addresses, and it still allows for later evolutionary processes.

[Civilized Worm]

It didn't turn into a horse therefore evolution is a lie!

[Kotatsu]

I stumbled across this (http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html)today, and would like verification. Specifically, I'm not familiar with New Scientist magazine, and I don't know how reliable a source they are. Would anyone care to comment?

I could get you the original article tomorrow, if you'd like. Or, at least, read it through and see what it's all about.

[Lanzy]

Its nice to post a link but a couple of words to let me know the subject would be nicer.

[Gord_in_Toronto]

It didn't turn into a horse therefore evolution is a lie!

And why are monkeys still around?

But seriously -- a very interesting piece of research and result. I can't wait to see the full analysis.

[CapelDodger]

Hats off to Lenski for setting up such a long-term experiment twenty years ago, which now appears to be bearing fruit. 44.000 generations, trillions of organisms, that's the sort of scale needed to reveal evolution in action. This could be big.

I've seen people argue that beneficial mutations are impossible because "information cannot be created"; this result refutes their logic and/or arithmetic entirely. Boo-yah!

[Showmeproof]

You can't prove that God doesn't exist, therefore he exists. Creationism for life!

Just like you can't prove that gnomes don't exist, therefore they exist.

http://www.youtube.com/watch?v=LAphcvZaS8I

[Jimbo07]

Pfah! It's just "micro" evolution... plus, Darwinists are liars... plus, the scientific establishment are Nazis... plus, physicists say the speed of light changes anyway, so why not 6000 years ago... plus, why do you hate America... ergo nothing in this study refutes Creation, as laid out in the Word by Him, in any way.

Plus a bunch of latin I learned at diploma-mill school:

ipso facto e puribus unum ad hominem ergo again morituri te salutant lookit me do philosophy ad nauseam...

[Mojo]

OMG! They've invented a strain of E. coli that can metabolise citrate! We're all doomed!

Seriously though, creationists will just say "it's only another sort of bacterium". Same kind, right?

[NobbyNobbs]

My question still stands....is this legit? Is this a reputable magazine? Do we finally have laboratory experiments we can point to and say "See? Told ya so!" ?

[Gord_in_Toronto]

My question still stands....is this legit? Is this a reputable magazine? Do we finally have laboratory experiments we can point to and say "See? Told ya so!" ?

The New Scientist is a recognized UK publication that has an international reputation for veracity.

Check it out here:
http://www.newscientist.com/news.ns

[Travis]

Don't we have poster on here that hates "New Scientist" with a vengeance?

[skeptigirl]

OMG! They've invented a strain of E. coli that can metabolise citrate! We're all doomed!

Seriously though, creationists will just say "it's only another sort of bacterium". Same kind, right?They can say it, but then they are ignorant about a lot of scientific facts.

It's being debated whether this represents a new species. Not only does it do something other e-coli do not, it also lost a characteristic, all other e-coli all have.

I'll have to review the article to give you the specifics.

[Patsy]

I can't imagine this will freak them out any more than everything else does.

Rational Person: Here is a large stack of scientific evidence that clearly shows your assertion the world is only 6000 years old is mistaken.

Creationist: I'm being persecuted! You hate Christians! It's a conspiracy!

RP: I think that only science should be taught in science classes. Religious and other values should be passed on at home in the family.

C: I'm being persecuted! You hate Christians! It's a conspiracy!

RP: Evolution has actually been observed in the laboratory.

C: I'm being persecuted! You hate Christians! It's a conspiracy.

No need to even change the script to handle this new information :D

[Wowbagger]

To most creationists, this will just be another example of "micro-evolution", I am sure. Not that such a distinction is real, but that seems to be how they dismiss all of these examples that crop up, every now and then.

Don't we have poster on here that hates "New Scientist" with a vengeance?
Well, It wouldn't be me, yet. I have only recently discovered how hideous New Scientist can be, sometimes. Give me more time to allow my hatred of the magazine to blossom.

[skeptigirl]

Found the whole article in a pdf file.

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli (http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf)

And here's Behe's comments (http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O) from his blog.I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.Here's your answer about what the Creationists will say. Ha! Talk about being unable to face the fact you have been wrong in a big way.

Behe is saying that the observation of a rare sequence of mutations occurring (needing to occur for species evolution), proves it can't happen. What an idiot.

[kellyb]

Found the whole article in a pdf file.

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli (http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf)

And here's Behe's comments (http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O) from his blog.Here's your answer about what the Creationists will say. Ha! Talk about being unable to face the fact you have been wrong in a big way.

Behe is saying that the observation of a rare sequence of mutations occurring (needing to occur for species evolution), proves it can't happen. What an idiot.

Hahaha...

[shadron]

Pfah! It's just "micro" evolution... plus, Darwinists are liars... plus, the scientific establishment are Nazis... plus, physicists say the speed of light changes anyway, so why not 6000 years ago... plus, why do you hate America... ergo nothing in this study refutes Creation, as laid out in the Word by Him, in any way.

Plus a bunch of latin I learned at diploma-mill school:

ipso facto e puribus unum ad hominem ergo again morituri te salutant lookit me do philosophy ad nauseam...

Are you sure that wasn't from Mel Brooks?

[shadron]

Don't we have poster on here that hates "New Scientist" with a vengeance?

Yes, I was about to cite Zosima; he has an avatar with a parody cover showing "Old Scientist". However, the point is more to whether the researchers are competent and can be trusted, IMO. I have no reason to believe they may not be.

[shadron]

I can't imagine this will freak them out any more than everything else does.

Rational Person: Here is a large stack of scientific evidence that clearly shows your assertion the world is only 6000 years old is mistaken.

Creationist: I'm being persecuted! You hate Christians! It's a conspiracy!

RP: I think that only science should be taught in science classes. Religious and other values should be passed on at home in the family.

C: I'm being persecuted! You hate Christians! It's a conspiracy!

RP: Evolution has actually been observed in the laboratory.

C: I'm being persecuted! You hate Christians! It's a conspiracy.

No need to even change the script to handle this new information :D

From a real, non-parody point of view, they do manage to ignore the nylonase mutation in bacteria, so I agree, this will not be a hurdle for them.

[Jimbo07]

Are you sure that wasn't from Mel Brooks?

You know, I'm amazed you've said just this! Just the other day I was looking at a Mel Brooks two 'fer movie pack...

It must be my inner Indigo child!

:D

[shadron]

OK, now, I have a philosophical question about this.

A while back, in a thread about SETI, The Atheist was citing the SETI program as borderline woo, because it is essentially an non-falsifiable experiment - actually he was railing about its cost, and this woo conjecture was a (semi-serious?) result. The SETI hypothesis, I imagine, can be expressed as "we think there are others out there", and they proceed to look, but no matter how hard they look, they won't ever be able to say, "Well, there must be none, because we have no positive results". While I don't agree with TA's conclusions, this presentation did make me stop and ponder a bit about the philosophy of the SETI project (hooray for the forum; at the very least, I'm entertained and find, surprising myself, that I can change opinions!).

Now we have Lenski's experiment. Very ambitious, and, in this case, very successful, or at least fraught with new lines of investigation, which is usually a sign of the same thing. I don't know what the object ("hypothesis") of the original experiment was, but I doubt it was to prove anything like the results we see here (or did it? Looking at the paper, they jump right into the citrate transport problem as if that was what they were hoping to see evolve from he first. Is that true?) I see philosophical parallels between SETI and Lenski's cultures, and I'm wondering how they should be regarded as science. I know of any number of experiments in which an instrument is built to observe some rare, perchance never occurring statistical event; is that essentially different from SETI?

Feel free to enlighten a dull engineer, if you please.

[shadron]

You know, I'm amazed you've said just this! Just the other day I was looking at a Mel Brooks two 'fer movie pack...

It must be my inner Indigo child!

:D

My teenaged kids have played all his movies so often that they are pretty much imprinted on my mind. When I was in college, one of the favorite pastimes among the theatre people (I was one of them, while pursuing physics) was dropping quotes from the play du jour into the conversaion, and I haven't been able to loose the knack, try as I might.

I was thinking of History of the World Part II, though the line also contained a lot of "bs, bs, bs...".

[shadron]

Wow. I'm beginning to feel as prolific as SkeptiGirl.... :D

[skeptigirl]

OK, now, I have a philosophical question about this.

A while back, in a thread about SETI, The Atheist was citing the SETI program as borderline woo, because it is essentially an non-falsifiable experiment - actually he was railing about its cost, and this woo conjecture was a (semi-serious?) result. The SETI hypothesis, I imagine, can be expressed as "we think there are others out there", and they proceed to look, but no matter how hard they look, they won't ever be able to say, "Well, there must be none, because we have no positive results". While I don't agree with TA's conclusions, this presentation did make me stop and ponder a bit about the philosophy of the SETI project (hooray for the forum; at the very least, I'm entertained and find, surprising myself, that I can change opinions!).

Now we have Lenski's experiment. Very ambitious, and, in this case, very successful, or at least fraught with new lines of investigation, which is usually a sign of the same thing. I don't know what the object ("hypothesis") of the original experiment was, but I doubt it was to prove anything like the results we see here (or did it? Looking at the paper, they jump right into the citrate transport problem as if that was what they were hoping to see evolve from he first. Is that true?) I see philosophical parallels between SETI and Lenski's cultures, and I'm wondering how they should be regarded as science. I know of any number of experiments in which an instrument is built to observe some rare, perchance never occurring statistical event; is that essentially different from SETI?

Feel free to enlighten a dull engineer, if you please.Since you've decided to take after one of the great web surfers (me) :D let me show you how the investigation is done.

I noticed the paper did say what the original problem was, I just wasn't familiar with the term, "historical contingency". I suspect you missed it as well.The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue.And since Lenski seemed to be mentioned more than the other authors, I just Googled, "Richard E. Lenski historical contingency". Then I opened the first few links that weren't just hits off the abstract. And I found the answer. [This search took 3 minutes, she joked after the Google acknowledgment they give themselves with every search. :)]

This link from Panda's Thumb had a clear answer.

Historical contingency in the evolution of E. coli (http://www.pandasthumb.org/archives/2008/06/historical-cont.html)What Blount et al. are doing is testing SJ Gould's old claim that if we replayed the tape of life, we would not get the same results each time. Each step in evolution is dependent on prior history — it is contingent — and since many of the steps are driven by chance yet unfiltered by selection, we cannot predict the direction of evolution.

We can't rewind the whole planet, but with careful design, we can set up populations that can be rewound. Lenski has done this by setting aside 12 separate populations of E. coli 20 years ago, each one evolving independently and in its own direction. So far, over 44,000 generations have passed in the flasks in Lenski's lab. This is a long time, and at the typical mutation rates present in these creatures, it means that every nucleotide has been mutated singly multiple times in the population — in other words, there has been ample time to thoroughly explore the single substitution search space. In addition, a sample of each population was taken and frozen every 500 generations, so they can go back in time at will and examine their genome or even restart the line. Imagine what we could learn if some ambiguously benevolent space aliens had visited the earth every 5-10,000 years, snatched up a couple of random hominin/primate tribes, and had them tucked away in cryogenic storage — that's what this experiment is like.


It's an excellent discussion and worth a look anyway.

[skeptigirl]

I love Panda's Thumb's comment on Behe's comments.Wait a minute — has he read the paper? This is an experiment that revealed a trait that required at least three mutations. Yet there it is, produced by natural evolution, with no intelligent design required; and when the experiment is re-run with populations that had the initial enabling variant, they re-evolved the ability multiple times. It seems to me that this work demonstrates that drift, chance, historical contingency, and selection are sufficient to overcome his "big evolutionary problem", and directly refute the premise of his book.It's so obvious to everyone except Behe.

[skeptigirl]

Here's Carl Zimmer's comments (http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php) on the research from a tip on Pharyngula. (http://scienceblogs.com/pharyngula/2008/06/release_the_hounds.php)

Be sure to read through the comments section of Zimmer's blog. One of the paper's authors is answering questions people post!

[shadron]

Since you've decided to take after one of the great web surfers (me) :D let me show you how the investigation is done.

Hey, one has to learn from the masters... ;)

I noticed the paper did say what the original problem was, I just wasn't familiar with the term, "historical contingency". I suspect you missed it as well.And since Lenski seemed to be mentioned more than the other authors, I just Googled, "Richard E. Lenski historical contingency". Then I opened the first few links that weren't just hits off the abstract. And I found the answer. [This search took 3 minutes, she joked after the Google acknowledgment they give themselves with every search. :)]

This link from Panda's Thumb had a clear answer.

Historical contingency in the evolution of E. coli (http://www.pandasthumb.org/archives/2008/06/historical-cont.html)

It's an excellent discussion and worth a look anyway.

Thanks for that; I'll read it. So, they weren't looking for anything in particular, just proof that contingency works as Gould said it would. I guess thay found proof with a vengence, then.

[CapelDodger]

Now we have Lenski's experiment. Very ambitious, and, in this case, very successful, or at least fraught with new lines of investigation, which is usually a sign of the same thing. I don't know what the object ("hypothesis") of the original experiment was, but I doubt it was to prove anything like the results we see here (or did it? Looking at the paper, they jump right into the citrate transport problem as if that was what they were hoping to see evolve from the first. Is that true?)

There's no other reason I can see for including citrate in the feed. E Coli is apparently known for its inability to metabolise citrate. This is what the scientists involved have been waiting for these past twenty years. It's a beautifully designed experiment. Hopefully it's not the only one started back in "the old days".

[Mashuna]

Apparently they'd thought that citrate metabolism was a possible bonus, but not explicitly what they were looking for. From the link skeptigirl gave in post 28, (scroll down to read post 115).

What is the citrate doing there? Well, it is part of the DM25 recipe, and has been since it was first reported by Bernard Davis and Elizabeth Mingioli in 1950 (Davis and Mingioli 1950. Mutants of Escherichia coli requiring methionine or vitamin B12. Journal of Bacteriology 60(1): 17 - 28.). They included it for two reasons. First, E. coli use something called the ferric di-citrate iron acquisition system to take up iron from their environment, though in this system, the citrate never enters the cell (see Hussein, S., Hantke, K., and Braun, V. 1981. Citrate-dependent iron transport system in Escherichia coli K-12. European Journal of Biochemistry, 117: 431 � 437.). While E. coli have another set of genes for what are called enterochelins, which can also be used for iron acquisition, citrate is commonly included in defined E. coli growth media (defined media are growth media for which we known exactly what is there and in what amount, as opposed to rich media such as Luria broth, trypticase soy broth, or brain heart infusion, which include enzymatic digests of yeasts and various proteins and, yes in the case of the third one, brains and hearts of cows which can vary in their exact constituents) just to make sure that the bacteria don't starve for iron. Also, when the media from which DM25 was developed were first formulated in the early to mid-20th century, it was common to keep them in 50x stocks that were then later diluted with water before use. At this concentration, the sodium citrate concentration was increased beyond what the organism strictly needed to prevent another component of the medium, magnesium sulfate, from precipitating out. As E. coli were not bothered by this, no other thought was given to the issue.

[Almo]

Great experiment. Seriously, great experiment. Another nail in the coffin of ID. You'd think there were enough by now, but we can keep putting more in. :)

[CapelDodger]

Apparently they'd thought that citrate metabolism was a possible bonus, but not explicitly what they were looking for. From the link skeptigirl gave in post 28, (scroll down to read post 115).

I'll take your word for it (and thanks); there's another reason for the citrate that I can now see. It's a necessary resource, but not as a food item.

Notice how that "possible bonus" seems to have paid out?

[CapelDodger]

Great experiment. Seriously, great experiment.

That bears repeating :).

And this experiment is by no means over.

[BeAChooser]

Very interesting article. Thanks.